I'm an atheist - the teacher said nothing wrong
Like the first movie, God's Not Dead 2 is also based on a false premise. Nothing the teacher said was against the law. If she were persecuted for what she did, I would've stood up for her... and I'm an atheist. The thing with the professor in the first movie would also never happen in real life.
Of course teachers can talk about Jesus if it has something to do with their class. They just can't evangelize and promote their own personal religious beliefs. Quoting and comparing Jesus' words in a history class is no different than quoting Zeus. But if she were to start saying how Zeus changed her life and that he answers your prayers, then that is a problem.
How would christians feel if a muslim teacher got up and said Muhammad is the only real prophet, and the Koran is the true word of Allah. I doubt christian parents would want their kids being told that in school. That is why the separation of church and state is important.
Sure, it's all ok when the government promotes christianity, but what happens when the tables turn and another religion gets more power and representation in the government? And they start making little changes like "one nation under Allah" and having muslim prayers before school starts. Christians would hit the roof and think the apocalypse is imminent. You can't have it both ways. The separation of church and state is GOOD for christians, not bad.